Question: Trimmomatic Error Message
0
gravatar for georgess.dan
14 months ago by
georgess.dan40
georgess.dan40 wrote:

Hello, Part of my Galaxy Workflow is to have Trimmomatic trim a FASTQsanger and to convert the output into a FASTQ.gz. Somewhere in the process, Trimmomatic gives the error pasted below. Does anyone know what this means? Is it not able to compress the output into fastq.gz?

Thanks,

Dan

Fatal error: Exit code 1 () Trimmomatic did not finish successfully The tool produced the following additional output: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/015/675/15675107/_galaxy_tmp -Xmx7680m -Xms256m TrimmomaticSE: Started with arguments: -threads 1 -phred33 fastq_in.fastq.gz fastq_out.fastq.gz SLIDINGWINDOW:4:20 Exception in thread "main" java.util.zip.ZipException: Not in GZIP format at java.util.zip.GZIPInputStream.readHeader(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:100) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:96) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.nextGzipInputStream(ConcatGZIPInputStream.java:38) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.<init>(ConcatGZIPInputStream.java:16) at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:140) at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:197) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:306)

at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

ADD COMMENTlink modified 14 months ago • written 14 months ago by georgess.dan40

This might be a case where the input was labeled as fastq.gz when it actually was simply fastq. Mismatches between the datatype and actual dataset content is problematic.

See the help here, make corrections if needed, rerun, and let us know what happened. If there is another error, we might ask you to send in a bug report.

Thanks, Jen, Galaxy team

ADD REPLYlink written 14 months ago by Jennifer Hillman Jackson25k

Hi Jen, As usual, thank you for your prompt reply. I read the information in the links you attached and curated all files names and attributes but the outcome was still the same (see error below). I think either there is something else that I'm doing wrong (and usually algorithms do not run if you don't provide them with proper input format) or Trimmomatic is being moody... Any help would be much appreciated! Thanks, Dan


Dataset generation errors Dataset 1: trimmedFastqSangerGZ

Tool execution generated the following error message: Fatal error: Exit code 1 () Trimmomatic did not finish successfully The tool produced the following additional output: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/015/678/15678452/_galaxy_tmp -Xmx7680m -Xms256m TrimmomaticSE: Started with arguments: -threads 1 -phred33 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:20 Exception in thread "main" java.util.zip.ZipException: Not in GZIP format at java.util.zip.GZIPInputStream.readHeader(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:100) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:96) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.nextGzipInputStream(ConcatGZIPInputStream.java:38) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.<init>(ConcatGZIPInputStream.java:16) at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:140) at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:197) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:306)

at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

ADD REPLYlink written 14 months ago by georgess.dan40
0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:

The bug report sent in helped, although I couldn't directly examine the dataset (it was not in the history, and that was permanently deleted anyway). I was able to trace back through the steps leading up to the job though, and it looks like the data was uncompressed at an intermediate step, but was still labeled as "fastqsanger.gz". Please double check this, rerun, and if that errors - please send in a complete, unaltered, undeleted History with all inputs/outputs included and we can look closer at full run details.

If there is a bug with using compressed inputs, we want to isolate it. I haven't been able to reproduce the problem in independent tests.

Thanks Dan! Jen

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson25k
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